This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The goal is to provide a combination of clustering plug-ins for the Cytoscape environment. Given an arbitrary weighted, undirected similarity graph (SG). This graph can be created for instance (i) by using the SFLDLoader, which queries the Structure Function Linkage Database, or (ii) by using all-vs.-all BLAST result files. Subsequently, special plug-ins may be used (i) to cluster the graph with Hierarchical Clustering (HC), Markov Clustering (MCL), Weighted Graph Cluster Editing (WGCE), and Connected Component analysis or (ii) to explore these clusters regarding several context-specific questions. Given a protein within a cluster, one might be interested in a list of clusters, ordered by protein-to-cluster similarities. Another example would be a scoring of all proteins within a given cluster regarding their similarity to all other elements (centrality analysis). One major goal of the ClusterExplorer is to assist with the manual post-annotation of SFLD data.